Error in `check_fields()`:
! Can't use fields that don't exist.
ℹ Use `search_all(fields)` to find a valid field ID.
✖ Can't find field(s) in
• `galah_group_by()`: species_guid
Fix
The species_facets function defined in R/utilities_internal.R needs to be updated as below
Better Fix
In a number of function, fields or a list of fields are being specified on a per LA instance basis. Instead of adding the field for individual atlas instances, maybe a column could be added to thedata-raw/node_config.csv file to indicate if the instance is using la-pipelines generated index or the legacy biocache-cli tool . This field could also be used in a similar situation in default_columns function in R/galah_select.R
Describe the bug galah
atlas_species()
function fails against LA instance with la-pipelines generated index (Sweden, France, Spain)galah version 2.0.1
To Reproduce Steps to reproduce the behaviour:
See error
Fix The
species_facets
function defined inR/utilities_internal.R
needs to be updated as belowBetter Fix In a number of function, fields or a list of fields are being specified on a per LA instance basis. Instead of adding the field for individual atlas instances, maybe a column could be added to the
data-raw/node_config.csv
file to indicate if the instance is using la-pipelines generated index or the legacy biocache-cli tool . This field could also be used in a similar situation indefault_columns
function inR/galah_select.R